Lab 9'4 RNA 25022004

1
RNA

• Département dInformatique et de Recherche
  Opérationnelle
• Université de Montréal
• C.P. 6128, Succursale Centre-Ville
• Montréal, Québec
• Canada H3C 3J7
• Francois.Major_at_UMontreal.CA

François Major
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TAR RNA in HIV-1

• The regulation of human immunodeficiency virus
  type 1 (HIV-1) gene expression is dependent on
  the transactivator protein Tat and an RNA element
  extending from the transcription initiation site
  to 57 known as TAR.
• TAR forms a stable RNA secondary structure which
  is critical for high levels of HIV-1 gene
  expression and efficient viral replication.

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TAR-RNA Structure
www.theochem.uni-frankfurt.de/ ygmu/
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A collection of TAR-RNA sequences(Tar_database2.t
xt)

• gtgi60192embZ11530.1HIVF12CG
  GACCAGATCTGAGCCTGGGAGCTCTCTGGCTA
• gtgi329369gbM93259.1HIVYU10XGACCAGATCTGAGCCTGG
  GAGCTCTCTGGCTA
• gtgi325586gbL02317.1HIV1SG3XGACCAGATCTGAGCCTGG
  GAGCTCTCTGGCTA
• gtgi1568309embA34828.1GACCAGATTTGAGCCTGGGAGCTC
  TCTGGCTA

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MFOLDhttp//www.bioinfo.rpi.edu/applications/mfol
d/old/rna
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MFOLD on UNIX

• Command line
• mfold SEQ'seq_mfold.txt
• gt
• GACCAGATCTGAGCCTGGGAGCTCTCTGGCTAltCRgt
• Tip Don't forget the ltreturngt at the end of
  your fasta formatted file !!!

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MFOLD OUTPUT (ct file)
velours.iro.umontreal.ca more myseq.ct 32
dG -10.6 initially -10.6 1 G 0
2 0 1 2 A 1 3 0 2 3
C 2 4 29 3 4 C 3 5
28 4 5 A 4 6 27 5 6 G
5 7 26 6 7 A 6 8 25
7 8 T 7 9 0 8 9 C 8
10 0 9 10 T 9 11 0 10
11 G 10 12 24 11 12 A 11 13
23 12 13 G 12 14 22 13 14 C
13 15 21 14 15 C 14 16 0
15 16 T 15 17 0 16 17 G 16
18 0 17 18 G 17 19 0 18
19 G 18 20 0 19 20 A 19 21
0 20 21 G 20 22 14 21 22 C
21 23 13 22 23 T 22 24 12
23 24 C 23 25 11 24 25 T 24
26 7 25 26 C 25 27 6 26
27 T 26 28 5 27 28 G 27 29
4 28 29 G 28 30 3 29 30 C
29 31 0 30 31 T 30 32 0
31 32 A 31 0 0 32
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MFOLD INPUT
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MFOLD SERVER OUTPUT
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Output in a Postcript file
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OUTPUT with RNAVIZ

• Command line gt rnaviz file.ct
• On server, choose RnaViz ct
• On Unix, choose your_file.ct

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PDB INPUT (1ANR)www.rcsb.org/pdb/
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PDB OUTPUT
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PDB OUTPUT (download)
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PDB file with RASMOL(rasmol 1ANR.pdb)
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McAnnotate INPUTwww-lbit.iro.umontreal.ca/mcanno
tate-simple/
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McAnnotate on UNIX

• Command line gt annotate 1ANR.pdb.gz

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McAnnotate Output
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ERPIN _at_ http//tagc.univ-mrs.fr/pub/erpin/

• Click on TAR, HIV-1
• Choose IRE, storage (for the assignment later)
• Parcourir the database Bank_test_Tar.cgi
  (include virus sequences)

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ERPIN on UNIX

• hiv_2.epn file
• gtstructure
• 00000000000000000000000000000000
• 11222223334444555555444422222666
• gtgi60192embz11530.1hivf12cg/1-32
• gaccagatctgagcctgggagctctctggcta
• gtgi329369gbm93259.1hivyu10x/1-32
• gaccagatctgagcctgggagctctctggcta
• gtgi325586gbl02317.1hiv1sg3x/1-32
• gaccagatctgagcctgggagctctctggcta
• gtgi1568309emba34828.1/1-32
• gaccagatttgagcctgggagctctctggcta

• Command line
• erpin hiv_2.epn ltdatabasegt 1,6 -cutoff 0 -nomask

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ERPIN RESULTS
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MC-Sym server (just for downloads)www-lbit.iro.um
ontreal.ca/mcsym/
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MC-Sym script

• sequence (r A1 CCAGA UCU GAGC CUGGGA GCUC
  UCUGG)residue( A1 A5 helix 1 A6 A8
  5 A9 A12 helix 1 A13 A18 C3p_endo
  anti 10 A19 A21 helix 1 A21 A22
  C3p_endo anti 10 A23 A27 helix
  1)connect( A1 A5 helix 1 A5 A9
  10 A9 A12 helix 1 A12 A19 5 A19
  A22 helix 1 A22 A23 15 A23 A27
  helix 1)

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MC-Sym script (suite)

• pair( A1 A27 wct 1 A2 A26 wct 1 A3
  A25 wct 1 A4 A24 wct 1 A5 A23 wct
  1 A9 A22 wct 1 A10 A21 wct 1 A11
  A20 wct 1 A12 A19 wct 1 )tar
  backtrackb( (A5 A23 A22 A9 A8 A7 A6) (A9 A10
  A21) (A10 A11 A20) (A11 A12 A19) (A12 A13
  A14 A15 A16 A17 A18) (A5 A4 A24) (A4 A3 A25)
  (A3 A2 A26) (A2 A1 A27))

• adjacency (tar 1.0 4.0)res_clash( tar
  fixed_distance 1 all no_hydrogen)explore(
  tar rmsd (1.0 pse_only) file_pdb
  ("PDB/tar-03d.pdb" zipped))

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MC-Sym on UNIX

• Command line gt mcsym tar.mcc

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One MC-Sym solution
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MC-RMS (Align mode)

• gt mcrms -s .pdb -o align.pdb

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MC-RMS (Classification mode)

• gt mcrms -sg .pdb